Create sof file with software inside

You don't want to use the JIC method in this case. Use the NIOS2 flash programmer accessible from within the Eclipse IDE. Select the option for programming your software project into flash and for programming an FPGA image into flash (you will have to browse to the compiled SOF file for your project). The NIOS2 flash programmer will program the FPGA image into the lowest address space of the EPCS flash and will program the software image immediately after the firmware FPGA image. The EPCS flash controller that you've placed in your SOPC system contains a bootloader that will automatically determine the size of the FPGA image, jump to the beginning of the software image and load the program into the RAM sections you've specified.